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Cenedril_Gildinaur
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Posted: Mon 11 Aug , 2008 6:07 pm
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The attempt to insert creationism through the free exercise clause instead of the establishment clause has failed. Religion doesn't belong in a science class, even as transfer credit.

MURRIETA: Judge throws out religious discrimination suit
Quote:
A federal judge in Los Angeles has thrown out the remaining claims of Calvary Chapel Christian School, which sued the University of California alleging university officials rejected some courses for credit because of their Christian viewpoint.

U.S. District Judge James Otero said in a summary judgment ruling released Friday that the school had failed to show evidence that UC officials had violated the First Amendment rights of the five Calvary students who sued along with the school and the Association of Christian Schools International.

Robert Tyler, an attorney who represented Calvary, said Friday night that the decision will be appealed.

"We always believed we were going to have to get up in the higher courts before we would get a ruling that would be favorable to us," said Tyler, general counsel for Advocates for Faith and Freedom, a religious liberty law firm in Murrieta.

In March, Otero threw out the Christian school's broader claims that UC policies were unconstitutional on their face. Friday's ruling concerned Calvary's claims that the policies were also unconstitutional as they were applied in the review of several classes.

Otero wrote that Calvary "provided no evidence of animus" on the part of university officials, whom he said had a "rational basis" for determining that the proposed Calvary courses would not meet the UC college preparatory requirements.
PDF of the Judge's ruling

Behe was an expert witness for the plaintiffs in this case, and got smacked down in the judge's ruling.
Quote:
Both professors concluded that neither the A Beka nor the BJU Biology texts are appropriate for use as the principal text in a college preparatory biology course. (Ayala Decl. Ex. A, at 28; Kennedy Decl. Ex. A, at 20.) In making this finding, Professor Kennedy reiterated Professor Sawrey's initial conclusion that "the problem is not . . . that the creationist view is taught as an alternative to scientific explanations, but that the nature of science, the theory of evolution, and critical thinking are not taught adequately." (Kennedy Decl. Ex. A, at 7.)

Plaintiffs offer little admissible evidence to the contrary. Plaintiffs' Biology expert, Dr. Michael Behe, submitted a declaration concluding that the BJU text mentions standard scientific content. (Watters Decl. Ex. U.) However, Professor Behe "did not consider how much detail or depth" the texts gave to this standard content. (Watters Decl. Ex. U ¶ 4.) Therefore, Professor Behe fails to refute one of Professor Kennedy's primary concerns that the nature of science, the theory of evolution, and critical thinking are not taught adequately.

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LalaithUrwen
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Posted: Mon 11 Aug , 2008 8:31 pm
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I think I had said earlier that this could be problematic for many, both homeschool and private kids. And I do have an issue with it. What exactly do they consider an adequate science text? Something they approve?

Major can of worms, there, imo.


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Cenedril_Gildinaur
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Posted: Tue 12 Aug , 2008 7:48 pm
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I imagine, given the 50 separate curricula in this country that they pretty much have to accept, the standards have to be pretty general. That this private school found a way to not meet those pretty general standards is more an indictment of the school than the university.

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It is a myth that coercion is necessary in order to force people to get along together, but it is a persistent myth because it feeds a desire many people have. That desire is to be able to justify hurting people who have done nothing other than offend them in some way.

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LalaithUrwen
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Posted: Wed 13 Aug , 2008 12:25 am
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Well, what concerns me is that the curricula they mentioned is very popular in Christian schools and with Christian homeschoolers. I mean, we're not talking about some obscure text printed by Joe Schmoe in his basement, though there are plenty of those. :suspicious: We are talking about A Beka and Bob Jones--two giants in the Christian curricula market!

I can sort of see their side of things on the science texts, though I still don't agree with the decision. The decision regarding history, though, is very troublesome. You don't like my interpretation of history? Well, I don't like yours. :shrug: I mean, I see this as an end-around on Christians (and it could be any religious group or any private group or family who has a different worldview than whatever is currently popular).

You don't want to attend our public schools and learn according to our secular, humanistic worldview? Okay, fine, but then we're going to say that your curricula is not good enough, and, therefore, your education is invalid.

I think that if a student can pass a test, do well on his SAT/ACT, prove himself to be a good citizen through whatever hoops he has to jump through, then that should be the criteria--not whether an institution happens to think that Bob Jones teaches history from a Christian worldview. Well, duh, of course they do. (And, honestly, to deny that this country was founded on Christian principles is absurd, but that is a different discussion.)

History, especially, is prone to being taught through the lenses of whatever view is currently in vogue.

Now, science, well, I know A Beka, but I haven't looked at the higher sciences to see how they treat the topic of evolution, i.e., how accurately they explain it. I think that if they give an accurate definition and explanation, then they are allowed (as a Christian text) to do what they want from there.

I know that will freak people out, and I know that people will abuse that. But I don't think the rights of people who won't abuse that should be curtailed in the theory that some people might.

Interestingly, I will be teaching biology this fall to the junior high kids in our co-op. I don't know how in-depth I'll be able to go, but I plan to give them an accurate description of evolution, as they would get it in a secular text. And I plan to discuss the fact that many Christians believe in evolution and all of that. IOW, I will do my best to present it as neutrally as possible. They need to know the facts behind this topic, not the hype (from either side).

ETA: I guess I should say that Ohio's law requires parents to provide the following: "Assurance that home education will include the following, except that home education shall not be required to include any concept, topic, or practice that is in conflict with the sincerely held religious beliefs of the parent." It goes on to list the following subjects: language, reading, spelling, and writing; geography, history of the US and Ohio, national, state, and local government; mathematics; science; health; PE; fine arts, including music; first aid, safety, and fire prevention.


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Jude
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Posted: Tue 25 Nov , 2008 1:47 pm
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Jude wrote:
Blasphemy Law may be abolished (UK)

:Q I didn't even know you guys still had a blasphemy law.


Get with the twenty-first century already, ok? :poke: :D
Well, to my great embarrassment, I find that Canada still has an anti-blasphemy law on the books.

It hasn't actually been used for 70 years, but still...

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Wolfgangbos
Post subject: Re: Back to the dark ages
Posted: Mon 12 Jan , 2009 5:42 pm
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http://www.scienceblog.com/cms/comment/reply/18191

From the article:

"[...] scientists have synthesized for the first time RNA enzymes that can replicate themselves without the help of any proteins or other cellular components, and the process proceeds indefinitely."

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Riverthalos
Post subject: Re: Back to the dark ages
Posted: Mon 12 Jan , 2009 6:20 pm
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Damn. This is one of the holy grails of in vitro evolution. A couple years ago Joyce came to my university to speak. At that point, they were getting close. And now they've got it.

I wish I could read the paper. Unfortunately, I can't get it off the Science website...and I'm on a university computer. WTF?

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Cenedril_Gildinaur
Post subject: Re: Back to the dark ages
Posted: Mon 12 Jan , 2009 10:18 pm
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River, cut and paste tiny text into some other document.

Scientists develop first examples of RNA that replicates itself indefinitely

One of the most enduring questions is how life could have begun on Earth. Molecules that can make copies of themselves are thought to be crucial to understanding this process as they provide the basis for heritability, a critical characteristic of living systems. Now, a pair of Scripps Research Institute scientists has taken a significant step toward answering that question. The scientists have synthesized for the first time RNA enzymes that can replicate themselves without the help of any proteins or other cellular components, and the process proceeds indefinitely.

The work was published on Thursday, January 8, 2009, in Science Express, the advanced, online edition of the journal Science.

In the modern world, DNA carries the genetic sequence for advanced organisms, while RNA is dependent on DNA for performing its roles such as building proteins. But one prominent theory about the origins of life, called the RNA World model, postulates that because RNA can function as both a gene and an enzyme, RNA might have come before DNA and protein and acted as the ancestral molecule of life. However, the process of copying a genetic molecule, which is considered a basic qualification for life, appears to be exceedingly complex, involving many proteins and other cellular components.

For years, researchers have wondered whether there might be some simpler way to copy RNA, brought about by the RNA itself. Some tentative steps along this road had previously been taken by the Joyce lab and others, but no one could demonstrate that RNA replication could be self-propagating, that is, result in new copies of RNA that also could copy themselves.
In Vitro Evolution

A few years after Tracey Lincoln arrived at Scripps Research from Jamaica to pursue her Ph.D., she began exploring the RNA-only replication concept along with her advisor, Professor Gerald Joyce, who is also dean of the faculty at Scripps Research. Their work began with a method of forced adaptation known as in vitro evolution. The goal was to take one of the RNA enzymes already developed in the lab that could perform the basic chemistry of replication, and improve it to the point that it could drive efficient, perpetual self-replication.

Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.

Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce's, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. "It kind of blew me away," says Lincoln.
Immortalizing Molecular Information

The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.

"This is the only case outside biology where molecular information has been immortalized," says Joyce.

Not content to stop there, the researchers generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such "mutations" occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. "To me that's actually the biggest result," says Joyce.

The research shows that the system can sustain molecular information, a form of heritability, and give rise to variations of itself in a way akin to Darwinian evolution. So, says Lincoln, "What we have is non-living, but we've been able to show that it has some life-like properties, and that was extremely interesting."
Knocking on the Door of Life

The group is pursuing potential applications of their discovery in the field of molecular diagnostics, but that work is tied to a research paper currently in review, so the researchers can't yet discuss it.

But the main value of the work, according to Joyce, is at the basic research level. "What we've found could be relevant to how life begins, at that key moment when Darwinian evolution starts." He is quick to point out that, while the self-replicating RNA enzyme systems share certain characteristics of life, they are not themselves a form of life.

The historical origin of life can never be recreated precisely, so without a reliable time machine, one must instead address the related question of whether life could ever be created in a laboratory. This could, of course, shed light on what the beginning of life might have looked like, at least in outline. "We're not trying to play back the tape," says Lincoln of their work, "but it might tell us how you go about starting the process of understanding the emergence of life in the lab."

Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. "We're knocking on that door," he says, "But of course we haven't achieved that."

The subunits in the enzymes the team constructed each contain many nucleotides, so they are relatively complex and not something that would have been found floating in the primordial ooze. But, while the building blocks likely would have been simpler, the work does finally show that a simpler form of RNA-based life is at least possible, which should drive further research to explore the RNA World theory of life's origins.

The paper is titled "Self-sustained Replication of an RNA Enzyme," and the work was supported by NASA and the National Institutes of Health, and the Skaggs Institute for Chemical Biology. For more information, see http://www.sciencemag.org/cgi/content/abstract/1167856" target="_blank" target="_blank" target="_blank.

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It is a myth that coercion is necessary in order to force people to get along together, but it is a persistent myth because it feeds a desire many people have. That desire is to be able to justify hurting people who have done nothing other than offend them in some way.

Last edited by Cenedril_Gildinaur on Tue Feb 30, 2026 13:61 am; edited 426 times in total


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Riverthalos
Post subject: Re: Back to the dark ages
Posted: Mon 12 Jan , 2009 10:39 pm
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Thanks CG, but I was referring to the actual research paper (I study RNA...need I say more?). The PDF is up on Science Express, but my university no longer holds an institutional subscription to Science Express so I can't download it like I could have a few weeks ago (apparently Science sells online access ala carte :roll:). I won a free two-year subscription, but that was two years ago and I think it's expired.

**grumbles and wanders off to find a friend with a subscription

ETA: my friend no longer has his subscription. I'll try my boss.

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LalaithUrwen
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 12:01 am
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I thought the same thing as CG at first, but then realized you were probably talking about the actual research paper. Let us know if you get access to it; I'd like to read it.


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Cenedril_Gildinaur
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 12:11 am
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Meh, I tried.

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It is a myth that coercion is necessary in order to force people to get along together, but it is a persistent myth because it feeds a desire many people have. That desire is to be able to justify hurting people who have done nothing other than offend them in some way.

Last edited by Cenedril_Gildinaur on Tue Feb 30, 2026 13:61 am; edited 426 times in total


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LalaithUrwen
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 12:21 am
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You did. :) And I nearly did the same thing.


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Riverthalos
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 12:42 am
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Eh, I wasn't being clear.

Anyway, my boss was able to download it. He sent me the PDF. If someone wants a copy, drop me a PM and I'll pass it along.

That said, it's not what the blog or the abstract led me to believe. I was expecting a full-on, bona fide ribozyme replicase that would copy one RNA into a new RNA using nucleotides. That's not what this is. This is a ligase - it staples together two pieces of already made RNA. The reason they call it self-replicating is because the ribozyme and the product mirror each other - ie, RNA A binds RNA B' and B" and catalyzes the joining of B' and B" into full length B. B will then turn around and bind A' and A" to form another A. That said, this is still very exciting because, unlike similar ribozymes that have been developed by in vitro evolution, this ribozyme turns over continuously. It does peter out or just act on itself once. It goes until it's out of material and then starts again when you give it more - they've got a beautiful curve. Exponential growth and then saturation unless they add more material. Thing is, it's slow - it takes 5 hours to reach saturation. Nevertheless, they got it to cook for 30 hours (I really hope Lincoln took her replicate data points in parallel because running that experiment even once had to suck) and then decided they'd made their point. Selecting a multiple turn-over ribozyme has been a huge hurdle and one of the reasons the nay-sayers to the RNA World hypothesis say nay. And now it's been shown to be possible. So that's pretty cool. They still need to come up with a real replicase though.

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Dave_LF
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 8:05 pm
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Computer scientists have been successfully using algorithms based on Darwinian evolution for quite some time, so there's no doubt that the idea itself is sound (i.e. reproduction + mutation + selection => automagic increase in fitness). I guess there'd be some value to verifying that it works in practice with actual biomolecules. It at least gives the biologists something to do.

(kidding, of course. I'm sure there are all sorts of neat things people could use that stuff for, only a few of which would ever occur to me).


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Riverthalos
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 8:18 pm
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Dave, most of the SELEX stuff being done right now breaks down into two categories: "Look what we can make RNA do!" and "Let's create an entirely RNA-based lifeform!" The former researchers try to sell as industrially or pharmaceutically applicable with some success. No chemical company is going to be using vats full of ribozyme to make products in the near future, but there is a RNA-based drug on the market and RNAs that were in vitro selected to bind certain small molecules are being developed as biosensors. Me, I can see uses for SELEX but, at the same time, my graduate work has been devoted to studying natural RNAs that selectively bind small molecules and honestly, nature does a much better job than us bench monkeys at selecting RNAs that detect small molecules and transduce a signal out of that binding event. If you want a biosensor, better to just get funky with natural riboswitches than start from scratch. And people are doing that.

The "Let's create an entirely RNA-based lifeform!" crowd are true believers in the RNA world and are trying to convince the rest of us we should believe too. I'm a bit non-plussed, though I'm not scientifically sold on the alternatives either. My preferred "How life began on Earth" bedtime story is we got seeded from space. An alien spacecraft, fleeing a dying sun, crashed here and we're the descendant of the surviving cell line. There's no evidence that this happened. It's just a fun story. But it's about as sensible as anything else and I like it because I'm a sci-fi fan.

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Dave_LF
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 8:31 pm
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Riverthalos wrote:
Me, I can see uses for SELEX but, at the same time, my graduate work has been devoted to studying natural RNAs that selectively bind small molecules and honestly, nature does a much better job than us bench monkeys at selecting RNAs that detect small molecules and transduce a signal out of that binding event. If you want a biosensor, better to just get funky with natural riboswitches than start from scratch. And people are doing that.
Do you think this or something like it might be a step toward artificially evolving RNA molecules to do whatever by letting these self-replicators run wild while imposing your own selective framework? I suppose you'd still at least want to start with a smattering of natural molecules that already do something similar to whatever you have in mind.


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Riverthalos
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 8:59 pm
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Well, in vitro selection of RNA (and even DNA) that does whatever has been around since the early '90's. The traditional method is to make a bunch of random sequences, subject them to your selection scheme, amplify the survivors, and repeat until things stop improving. I suppose you could use these self-replicators as a chassis if you wanted, say, a RNA that replicated in response to something. Interestingly, it was the development of in vitro selected RNAs that were capable of binding small molecules that led to the discovery of natural RNAs that could do the same thing. The first natural sequences tested for this capability had been known of for years but their purpose wasn't understood until someone had a leap of insight and did the experiment. There's nothing new about these natural sequences - at least one has been around since the last universal common ancestor - but no one recognized them for what they were until ~2002.

Generally, in vitro selection experiments are not doped with natural sequence though sometimes you'll see people randomize chunks of natural sequence and run selections on that. Usually, those sorts of experiments are done to determine the binding sites for certain proteins (in fact, the first SELEX experiment ever performed was for that reason).

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Dave_LF
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 10:00 pm
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Very interesting. Theoretically I should already have known that, but somewhere along the line I became a computer scientist who knows about biology rather than a biologist who knows about computer science. Stop me if this is getting too long, but would I be correct guessing that "imposing your selection scheme" is the hardest part of the design? It's easy to say "remove a molecule with a probability that is inversely proportional to the degree to which it has bonded to the target ligand", but I can't begin to imagine how you'd actually do it. That's one of the things I enjoy about programming, by the by; saying and doing are the same thing. You have merely to speak (type) it, and it is so.


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Riverthalos
Post subject: Re: Back to the dark ages
Posted: Tue 13 Jan , 2009 10:14 pm
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Yes, the selection scheme is the hard part. It's doable, but one of the limiting factors in in vitro selection is the quality of the selection techniques. There was a time when I wanted to do in vitro selections, but then riboswitches hit the scene and nature does such a good job at selecting RNAs that bind specific molecules I decided to just study those.

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LalaithUrwen
Post subject: Re: Back to the dark ages
Posted: Sat 07 Feb , 2009 4:06 am
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Okay, so I read something today that actually seemed logical and possible to me regarding evolution.
Quote:
Evolution works not just by changing genes, but by modifying the way those genes are switched on and off. ..."The primary fuel for the evolution of anatomy turns out not to be gene changes, but changes in the regulation of genes that control development."

The notion of genetic switches explains the humiliating surprise that human beings appear to have no special human genes. Over the past decade, as scientists compared the human genome with that of other creatures, it has emerged that we inherit not just the same number of genes as a mouse--fewer than 21,000--but in most cases the very same genes. Just as you don't need different words to write different books, so you don't need new genes to make new species: You just change the order and pattern of their use.
example:
Quote:
...the researchers studied a living proxy--a primitive bony fish called a paddlefish--and found that the pattern of gene expression that builds the bones in its fins is much the same as the one that assembles the limb in an embryo of a bird, a mammal, or any other land-living animal. The difference is only that it is switched on for a shorter time in fish. The discovery overturned a long-held notion that the acquisition of limbs required a radical evolutionary event.
Now, this, to me has some merit. The genes are all there; the controls are different.

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